non-target RNA-Seq in Ribo-STAMP-293T

General Information

List KD experiments controlled by BGRSDTLV02-1tot and BGRSDTLV02-2tot

NT-BGRSDTLV02-1tot,NT-BGRSDTLV02-2tot:

Experiment Information (Status: Submitted)

	BGRSDTLV02-1tot	BGRSDTLV02-2tot
idx	0	0
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGRSDTLV02-1tot	BGRSDTLV02-2tot
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note	sample experiment in BGRSDLV02, Total-RNA	sample experiment in BGRSDLV02, Total-RNA
ID	9306	9307

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDTLV02-1tot	BGRSDTLV02-2tot
Sample_ID	BGRSDTLV02-1tot	BGRSDTLV02-2tot
Sample Name
Sample Name	NT-BGRSDTLV02-1tot	NT-BGRSDTLV02-2tot
RBP	non-target	non-target
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12412	12413

Library-Prep
Sequencing

Library-Prep Information

	BGRSDTLV02-1tot	BGRSDTLV02-2tot
Sample #	77	78
Sample Name	NT-BGRSDTLV02-1tot	NT-BGRSDTLV02-2tot
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-27	2023-09-27
Lib_ID	Lib-230927	Lib-230927
Tecan_Location
Tecan
Tecan_date
Size_bp	266	266
Peak_Molarity	2.77	1.83
libSampleQC_DNA_Well	DNA_Library_set65_tot/set1/A11.png	DNA_Library_set65_tot/set1/B11.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set65/set1/A1.png	RNA_Library_set65/set1/B1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-03	2023-10-03
Sample_ID	BGRSDTLV02-1tot	BGRSDTLV02-2tot
RBP	NT	NT
Batch_ID	BGRSDTLV02	BGRSDTLV02
WB_result	0.000	0.000
Library Description	TruSeq Total RNA	TruSeq Total RNA
Repeat_Library_Suffix	t	t
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3998	3999

Sequencing Information

	BGRSDTLV02-1tot	BGRSDTLV02-2tot
Sample_ID	BGRSDTLV02-1tot	BGRSDTLV02-2tot
Sample Name	NT-BGRSDTLV02-1tot	NT-BGRSDTLV02-2tot
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65_tot	set65_tot
total_reads	31,014,796	46,510,443
total_aligned_reads	18,829,804	31,706,328
unique_aligned_reads	17,186,019	29,463,095
percent_uniqueAligned	0.55412	0.63347
correlation_replicates	0.953869	0.953869
spikein_reads	55,086	118,304
percent_spikeins	0.00178	0.00254
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2745	2746

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	Project	FILE_ID
NT-BGRSDTLV02-1tot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2745	NovaSeq6000	100	paired-ended	1				ENCORE2	8890
NT-BGRSDTLV02-1tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2745	NovaSeq6000	100	paired-ended	2				ENCORE2	8898
NT-BGRSDTLV02-1tot_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2745					GRCh38	V40	NT-BGRSDTLV02-1tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-1tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9255
NT-BGRSDTLV02-1tot_Signal.Unique.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2745					GRCh38	V40	NT-BGRSDTLV02-1tot/Aligned.sortedByCoord.out.bam	ENCORE2	9263
NT-BGRSDTLV02-1tot_Signal.Unique.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2745					GRCh38	V40	NT-BGRSDTLV02-1tot/Aligned.sortedByCoord.out.bam	ENCORE2	9271
NT-BGRSDTLV02-1tot_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2745					GRCh38	V40	NT-BGRSDTLV02-1tot/Aligned.sortedByCoord.out.bam	ENCORE2	9279
NT-BGRSDTLV02-1tot_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2745					GRCh38	V40	NT-BGRSDTLV02-1tot/Aligned.sortedByCoord.out.bam	ENCORE2	9287
NT-BGRSDTLV02-1tot_quant.sf	ENCODE_DATA/set65_tot/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2745					GRCh38	V40	NT-BGRSDTLV02-1tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-1tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9295
NT-BGRSDTLV02-2tot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2746	NovaSeq6000	100	paired-ended	1				ENCORE2	8891
NT-BGRSDTLV02-2tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2746	NovaSeq6000	100	paired-ended	2				ENCORE2	8899
NT-BGRSDTLV02-2tot_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2746					GRCh38	V40	NT-BGRSDTLV02-2tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-2tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9256
NT-BGRSDTLV02-2tot_Signal.Unique.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2746					GRCh38	V40	NT-BGRSDTLV02-2tot/Aligned.sortedByCoord.out.bam	ENCORE2	9264
NT-BGRSDTLV02-2tot_Signal.Unique.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2746					GRCh38	V40	NT-BGRSDTLV02-2tot/Aligned.sortedByCoord.out.bam	ENCORE2	9272
NT-BGRSDTLV02-2tot_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2746					GRCh38	V40	NT-BGRSDTLV02-2tot/Aligned.sortedByCoord.out.bam	ENCORE2	9280
NT-BGRSDTLV02-2tot_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2746					GRCh38	V40	NT-BGRSDTLV02-2tot/Aligned.sortedByCoord.out.bam	ENCORE2	9288
NT-BGRSDTLV02-2tot_quant.sf	ENCODE_DATA/set65_tot/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2746					GRCh38	V40	NT-BGRSDTLV02-2tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-2tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9296